Sounds like something I've experienced before. It usually comes down to needing new shoes. I'm knock-kneed so have always walked a little bit awkward. I've noticed that I wear down shoes in a strange way, so that the inside of my foot (edge by big toe) wears down faster than the outside. Think of it instead of standing flat, my feet start making a V shape after a while, which seems to put strain on my ankles and soles if I keep wearing them.
Sounds like the same type of thing as you. Don't notice it when I'm walking around, but it kicks in after I stand up if I've been sitting for a bit.
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